@sladflob: Whatever you put inside .kobo that shouldn't be in there
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Note that seeing KOReader's icons being indexed by Nickel happens to be a new feature of FW 4.17+, which might confuse the issue some more (especially if seeing those icons getting indexed is what made you think "uh oh, I messed up". So, did you actually unpack stuff in the wrong place?).
Quote:
Originally Posted by NiLuJe
NOTE: On FW 4.17+, you'll probably also want to prevent Nickel from scanning *nix hidden folders. And you'll want to tweak your config before unplugging your device (i.e., before installing this; or, if you've just upgraded your FW, during the first USB connection after the update).
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And, yes, doing that after the fact will cause Nickel to delete the files, so you'll have to reinstall KOReader.
Hence the emphasis on doing it right the first time around and in the right order
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TL;DR: Use the install script ;p.